Molecular Mapping and Breeding with Microsatellite Markers

Abstract

In genetics databases for crop plant species across the world, there are thousands of mapped loci that underlie quantitative traits, oligogenic traits, and simple traits recognized by association mapping in populations. The number of loci will increase as new phenotypes are measured in more diverse genotypes and genetic maps based on saturating numbers of markers are developed. A period of locus reevaluation will decrease the number of important loci as those underlying mega-environmental effects are recognized. A second wave of reevaluation of loci will follow from developmental series analysis, especially for harvest traits like seed yield and composition. Breeding methods to properly use the accurate maps of QTL are being developed. New methods to map, fine map, and isolate the genes underlying the loci will be critical to future advances in crop biotechnology. Microsatellite markers are the most useful tool for breeders. They are codominant, abundant in all genomes, highly polymorphic so useful in many populations, and both economical and technically easy to use. The selective genotyping approaches, including genotype ranking (indexing) based on partial phenotype data combined with favorable allele data and bulked segregation event (segregant) analysis (BSA), will be increasingly important uses for microsatellites. Examples of the methods for developing and using microsatellites derived from genomic sequences are presented for monogenic, oligogenic, and polygenic traits. Examples of successful mapping, fine mapping, and gene isolation are given. When combined with high-throughput methods for genotyping and a genome sequence, the use of association mapping with microsatellite markers will provide critical advances in the analysis of crop traits.

Root system architecture, physiological and transcriptional traits of soybean (Glycine max L.) in response to water deficit: A review

“…In recent years, with the rapid development of simple sequence repeats (SSR) marker technology, a variety of molecular markers have been widely used in soybean yield traits and correlation analysis (Galeano et al 2012, He et al 2012, Lightfoot and Iqbal 2013). Ning et al (2017) studied the polymorphism of 36 soybean cultivars under drought and high temperature treatments and detected 156 alleles in 49 polymorphic markers.…”

Genome-Wide Mining, Characterization and Development of miRNA-SSRs inArabidopsis thaliana

“…SSRs are co-dominant, and multi-allelic by nature and due to constant variation in the number of tandem repeats; they are known to be, robust, highly polymorphic (Brandstrom et al 2008, Heesacker et al 2008), locus-specific and co-dominant, thus becoming the markers of choice. (Gupta et al 1996; Ni et al 2002; Lightfoot and Iqbal, 2013; Senan et al 2014; Wang et al 2015). Previous reports show that SSRs are selectively neutral and are randomly distributed in the eukaryotic genome (Schlotterer, 2000; Schlotterer, 2004).…”